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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structure and Function of REP34 Implicates Carboxypeptidase Activity in Francisella tularensis Host Cell Invasion

Francisella tularensis is the etiological agent of tularemia, or rabbit fever. Although F. tularensis is a recognized biothreat agent with broad and expanding geographical range, its mechanism of infection and environmental persistence remain poorly understood. Previously, we identified seven F. tularensis proteins that induce a rapid encystment phenotype (REP) in the free-living amoeba, Acanthamoeba castellanii. Encystment is essential to the pathogen's long term intracellular survival in the amoeba. Here, we characterize the cellular and molecular function of REP34, a REP protein with a mass of 34 kDa. A REP34 knock-out strain of F. tularensis has a reduced ability to both induce encystment in A. castellanii and invade human macrophages. We determined the crystal structure of REP34 to 2.05-Å resolution and demonstrate robust carboxypeptidase B-like activity for the enzyme. REP34 is a zinc-containing monomeric protein with close structural homology to the metallocarboxypeptidase family of peptidases. REP34 possesses a novel topology and substrate binding pocket that deviates from the canonical funnelin structure of carboxypeptidases, putatively resulting in a catalytic role for a conserved tyrosine and distinct S1' recognition site. Taken together, these results identify REP34 as an active carboxypeptidase, implicate the enzyme as a potential key F. tularensis effector protein, and may help elucidate a mechanistic understanding of F. tularensis infection of phagocytic cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

One fold, many functions—M23 family of peptidoglycan hydrolases

Bacterial cell walls are the guards of cell integrity. They are composed of peptidoglycan that provides rigidity to sustain internal turgor and ensures isolation from the external environment. In addition, they harbor the enzymatic machinery to secure cell wall modulations needed throughout the bacterial lifespan. The main players in this process are peptidoglycan hydrolases, a large group of enzymes with diverse specificities and different mechanisms of action. They are commonly, but not exclusively, found in prokaryotes. Although in most cases, these enzymes share the same molecular function, namely peptidoglycan hydrolysis, they are leveraged to perform a variety of physiological roles. A well-investigated family of peptidoglycan hydrolases is M23 peptidases, which display a very conserved fold, but their spectrum of lytic action is broad and includes both Gram- positive and Gram- negative bacteria. In this review, we summarize the structural, biochemical, and functional studies concerning the M23 family of peptidases based on literature and complement this knowledge by performing large-scale analyses of available protein sequences. This review has led us to gain new insight into the role of surface charge in the activity of this group of enzymes. We present relevant conclusions drawn from the analysis of available structures and indicate the main structural features that play a crucial role in specificity determination and mechanisms of latency. Our work systematizes the knowledge of the M23 family enzymes in the context of their unique antimicrobial potential against drug-resistant pathogens and presents possibilities to modulate and engineer their features to develop perfect antibacterial weapons.

Razew, Alicja↗
DOE OSTI2023

Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs

RNA polymerase (RNAP) is emblematic of complex biological systems that control multiple traits involving trade-offs such as growth versus maintenance. Laboratory evolution has revealed that mutations in RNAP subunits, including RpoB, are frequently selected. However, we lack a systems view of how mutations alter the RNAP molecular functions to promote adaptation. We, therefore, measured the fitness of thousands of mutations within a region of rpoB under multiple conditions and genetic backgrounds, to find that adaptive mutations cluster in two modules. Mutations in one module favor growth over maintenance through a partial loss of an interaction associated with faster elongation. Mutations in the other favor maintenance over growth through a destabilized RNAP-DNA complex. The two molecular handles capture the versatile RNAP-mediated adaptations. Combining both interaction losses simultaneously improved maintenance and growth, challenging the idea that growth-maintenance tradeoff resorts only from limited resources, and revealing how compensatory evolution operates within RNAP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

High throughput, accurate gene annotation through AI and HPC-enabled structural analysis

With the advances in next generation sequencing technologies, the number of sequenced genomes is growing exponentially, resulting in a technology bottleneck for the translation of sequence information into usable hypotheses about the function of each gene. We have proposed leveraging our leadership high-performance computing (HPC) resources to help break this annotation bottleneck. Here we design an HPC-based framework to infer gene function from gene sequence by incorporating information about protein structure and interactions predicted by deep learning approaches. Accurate functional prediction and gene annotation using computational methods will facilitate breakthroughs in the genomic sciences essential to understanding and harnessing life processes in bacteria, fungi and plants. The development and applications of the state-of-the-art deep neural networks to protein structural modeling, interaction prediction, sequence comparison, and quality assessment of protein structural models will be made possible by leadership computational resources. These HPC-enabled bioinformatics and molecular modeling tools will provide powerful insights into molecular functions of genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Synergistic Density Functional Theory and Molecular Dynamics Approach to Elucidate PNIPAM–Water Interaction Mechanisms

This study employs Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations to investigate interactions between water molecules and Poly(N-isopropylacrylamide) (PNIPAM). DFT reveals preferential water binding sites, with enhanced binding energy observed in the linker zone. Quantum Theory of Atoms in Molecules (QTAIM) and electron localization function (ELF) analyses highlight the roles of hydrogen bonding and steric hindrance. MD simulations unveil temperature-dependent hydration dynamics, with structural transitions marked by changes in the radius of gyration (Rg) and the radial distribution function (RDF), aligning with DFT findings. Our work goes beyond prior studies by combining a DFT, QTAIM and MD simulations approach across different PNIPAM monomer-to-30mer structures. It introduces a systematic quantification of pseudo-saturation thresholds and explores water clustering dynamics with structural specificity, which have not been previously reported in the literature. These novel insights establish a more complete molecular-level picture of PNIPAM hydration behavior and temperature responsiveness, emphasizing the importance of amide hydrogen and carbonyl oxygen sites in hydrogen bonding, which weakens above the lower critical solution temperature (LCST), resulting in increased hydrophobicity and paving the way for understanding water sorption mechanisms, offering guidance for future applications such as dehumidification and atmospheric water harvesting.

08 HYDROGEN↗
DOE OSTI2025

High‐Temperature Single‐Photon Emission From Covalently Functionalized van der Waals Heterostructures

Two-dimensional (2D) transition metal dichalcogenides (TMDs) such as tungsten diselenide (WSe 2 ) are attractive nanomaterials for quantum information applications due to single-photon emission (SPE) from intrinsic atomic defects. Defect and strain engineering techniques have been developed to produce high purity, deterministically placed SPE in WSe 2 . However, a major challenge in the application of these techniques is the low temperature required to observe defect-bound TMD exciton emission, typically limiting SPE to T < 30 K. SPE at higher temperatures either loses purity or requires integration into complex devices such as optical cavities. Here, 2D heterostructure engineering and molecular functionalization are combined to achieve high purity (>90%) SPE in strained WSe 2 persisting to over T = 90 K. Covalent diazonium functionalization of graphite in layered WSe 2 /graphite heterostructures maintains high purity up to T = 90 K and single-photon source integrity up to T = 115 K. This method preserves the best qualities of SPE from WSe 2 while increasing working temperature to more than three times the typical range. This work demonstrates the versatility of surface functionalization and heterostructure design to synergistically improve the properties of quantum emission and offers new insights into the phenomenon of SPE from 2D materials.

2D materials↗
DOE OSTI2022

Thickness-dependent spin bistable transitions in single-crystalline molecular 2D material

Abstract The advent of two-dimensional (2D) crystals has led to numerous scientific breakthroughs. Conventional 2D systems have in-plane covalent bonds and a weak out-of-plane van-der-Waals bond. Here we report a new type of 2D material composed of discrete magnetic molecules, where anisotropic van-der-Waals interactions bond the molecules into a 2D packing. Through mechanical exfoliation, we can obtain single-crystalline molecular monolayers, which can be readily integrated into other 2D systems. Optical spectroscopy suggests the few-layered molecules preserve the temperature-induced spin-crossover switching observed in the bulk form but show a drastic increase in thermal hysteresis unique to these thin 2D molecule assemblies. The trapping of spin bistability with decreasing layer number can arise from domain wall dynamics in reduced dimensions. Our results establish molecular solids with strong anisotropy of intermolecular interactions as precursors to a new class of 2D materials, affording possibilities to control molecular functionalities through substrate and interlayer interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Anharmonicity and Phase Diagram of Magnesium Oxide in the Megabar Regime

With density functional molecular dynamics simulations, we computed the phase diagram of MgO from 50 to 2000 GPa up to 20000 K. Via thermodynamic integration (TDI), we derive the Gibbs free energies of the B1, B2, and liquid phases and determine their phase boundaries. With TDI and a pseudo-quasi-harmonic approach, we show that anharmonic effects are important and stabilize the B1 phase in particular. As a result, the B1-B2 transition boundary in the pressure-temperature plane exhibits a steep slope. We predict the B1-B2-liquid triple point to occur at approximately T= 10000 K and P = 370 GPa, which is higher in pressure than was inferred with quasi-harmonic methods alone. We predict the principal shock Hugoniot curve to enter the B2 phase stability domain but only over a very small range of parameters. Here, this may render it difficult to observe this phase with shock experiments because of kinetic effects.

3-dimensional systems↗
DOE OSTI2024

Structure analysis of the telomere resolvase from the Lyme disease spirochete Borrelia garinii reveals functional divergence of its C-terminal domain

Borrelia spirochetes are the causative agents of Lyme disease and relapsing fever, two of the most common tick-borne illnesses. A characteristic feature of these spirochetes is their highly segmented genomes which consists of a linear chromosome and a mixture of up to approximately 24 linear and circular extrachromosomal plasmids. The complexity of this genomic arrangement requires multiple strategies for efficient replication and partitioning during cell division, including the generation of hairpin ends found on linear replicons mediated by the essential enzyme ResT, a telomere resolvase. Using an integrative structural biology approach employing advanced modelling, circular dichroism, X-ray crystallography and small-angle X-ray scattering, we have generated high resolution structural data on ResT from B. garinii. Our data provides the first high-resolution structures of ResT from Borrelia spirochetes and revealed active site positioning in the catalytic domain. We also demonstrate that the C-terminal domain of ResT is required for both transesterification steps of telomere resolution, and is a requirement for DNA binding, distinguishing ResT from other telomere resolvases from phage and bacteria. These results advance our understanding of the molecular function of this essential enzyme involved in genome maintenance in Borrelia pathogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Chemical Insights into the Molecular Composition of Organic Aerosols in the Urban Region of Houston, Texas

Molecular functional groups, such as organosulfates (CHOS) and organonitrates (CHNO) are important tracers for field observations of secondary organic aerosols (SOA). While CHOS and CHNO are prevalent in the atmosphere, there is a lack of knowledge regarding daily and day- and night-time variations in these species in the urban atmosphere. Meteorological factors such as wind speed/direction, relative humidity (RH), and temperature can influence the formation of CHOS/CHNO. To investigate these trends, we utilized multimodal chemical imaging and advanced high resolution mass spectrometry techniques to acquire particle speciation and molecular formulas (MFs) associated with day and night sampling periods. Back trajectory analyses revealed the oceanic influence of southern wind airmasses in later June sampling periods with organic fractions <10%. Conversely, northern winds in early June sampling periods contributed to the episodic emergence of extremely low volatile organics (ELVOCs) and organic factions up to 41%. The observed unique MFs to June 3 (223 MFs) and to June 4 (144 MFs) were largely found to be of biogenic rather than anthropogenic origin. Finally, our findings reveal episodic prevalence and temporal distribution of SOA constituents across the urban region of Houston, Texas.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Ultrafast X-Ray Probes of Elementary Molecular Events

Elementary events that determine photochemical outcomes and molecular functionalities happen on the femtosecond and subfemtosecond timescales. Among the most ubiquitous events are the nonadiabatic dynamics taking place at conical intersections. These facilitate ultrafast, nonradiative transitions between electronic states in molecules that can outcompete slower relaxation mechanisms such as fluorescence. The rise of ultrafast X-ray sources, which provide intense light pulses with ever-shorter durations and larger observation bandwidths, has fundamentally revolutionized our spectroscopic capabilities to detect conical intersections. Recent theoretical studies have demonstrated an entirely new signature emerging once a molecule traverses a conical intersection, giving detailed insights into the coupled nuclear and electronic motions that underlie, facilitate, and ultimately determine the ultrafast molecular dynamics. Following a summary of current sources and experiments, we survey these techniques and provide a unified overview of their capabilities. We discuss their potential to dramatically increase our understanding of ultrafast photochemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

ACBD3 is up-regulated in gastric cancer and promotes cell cycle G1-to-S transition in an AKT-dependent manner

Highlights: • ACBD3 is up-regulated in gastric cancer. • ACBD3 regulates cell-cycle of gastric cancer in an AKT-dependent manner. It has been reported that ACBD3 is closely related to the malignant process of cells, but its role in gastric cancer has not been elucidated. This study aims to investigate the expression and function of ACBD3 in human gastric cancer. The Cancer Genome Atlas (TCGA) database were selected to analyze mRNA levels of ACBD3 in gastric cancer tissues and normal gastric epithelial tissues. qPCR and Western blot were conducted to detect the expression of ACBD3 in two normal gastric epithelial cell lines and five gastric cancer cell lines which were cultured in our laboratory. To exclude differences in individual background between different patients, we further detected the expression of ACBD3 in 8 pairs of malignant/non-malignant clinical gastric tissues. Through the establishment of stable cells, in vitro cell experiments and in vivo xenotransplantation models in mice, the role of ACBD3 in the proliferation of gastric cancer cells has been further explored. AKT inhibitors were used to deeply explore the molecular regulation mechanism of ACBD3. The results showed that the elevated ACBD3 in gastric cancer tissue were positively correlated with the clinical grade and prognosis of gastric cancer. In terms of molecular function, we found that ACBD3 can enhance the production and growth of gastric cancer cells. At the same time, the activation of AKT kinase played an important role in ACBD3's promotion of G1-to-S transition. The experiments generally indicate that ACBD3 is expected to become a potential diagnostic molecule or therapeutic target for gastric cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

First-principles equation of state database for warm dense matter computation

We put together a first-principles equation of state (FPEOS) database for matter at extreme conditions by combining results from path integral Monte Carlo and density functional molecular dynamics simulations of the elements H, He, B, C, N, O, Ne, Na, Mg, Al, and Si as well as the compounds LiF , B 4 C , BN , CH 4 , CH 2 , C 2 H 3 , CH , C 2 H , MgO , and MgSiO 3 . For all these materials, we provide the pressure and internal energy over a density-temperature range from ~ 0.5 to 50 g cm - 3 and from ~ 10 4 to 10 9 K, which are based on ~ 5000 different first-principles simulations. We compute isobars, adiabats, and shock Hugoniot curves in the regime of L - and K -shell ionization. Invoking the linear mixing approximation, we study the properties of mixtures at high density and temperature. Furthermore, we derive the Hugoniot curves for water and alumina as well as for carbon-oxygen, helium-neon, and CH-silicon mixtures. We predict the maximal shock compression ratios of H 2 O , H 2 O 2 , Al 2 O 3 , CO , and CO 2 to be 4.61, 4.64, 4.64, 4.89, and 4.83, respectively. Finally we use the FPEOS database to determine the points of maximum shock compression for all available binary mixtures. We identify mixtures that reach higher shock compression ratios than their end members. We discuss trends common to all mixtures in pressure-temperature and particle-shock velocity spaces. In the Supplemental Material, we provide all FPEOS tables as well as computer codes for interpolation, Hugoniot calculations, and plots of various thermodynamic functions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Newly developed sugarbeet lines with altered postharvest respiration rates differ in transcription factor and glycolytic enzyme expression

Respiration is the principal cause for postharvest sucrose loss in sugarbeet (Beta vulgaris L.) roots. Although reductions in respiration rate could mitigate these losses, developing sugarbeet cultivars and storage procedures that reduce respiration are hindered by a lack of knowledge of the genetic and metabolic factors that control storage respiration rate. Research was conducted to identify genes and gene products that affect storage respiration rate by creating two sugarbeet lines that differ in respiration rate and characterizing gene expression differences between these lines. Sugarbeet lines F1056 and F1057, which differ by up to 42% in respiration rate, were created by divergent selection of a sugarbeet population using root respiration rate after 30 d in storage as the principal selection criterion. RNA sequencing identified 287 differentially expressed genes (DEGs) between these lines on the day of harvest and after 28-d storage. Of these DEGs, nine encoded transcription factors and five encoded enzymes involved in the respiratory pathway. Other DEGs contributed to a variety of biological and molecular functions based on gene ontology classifications. Of respiratory pathway DEGS, genes for NAD+- and NADP+-dependent forms of glyceraldehyde-3-phosphate dehydrogenase were of note due to their high upregulation in the high respiring line and for their established role in glycolysis, a pathway identified as a likely bottleneck in respiratory substrate production. Overall, lines F1056 and F1057 provide new tools for investigating genetic and physiological differences in storage respiration rate, and their DEGs identify candidates for genes affecting sugarbeet root respiration rate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The homogeneous mixing of MgO and H 2 O at extreme conditions

Investigating water worlds presents a unique opportunity to understand the fundamental processes of planetary formation and evolution. One key aspect is characterizing the interactions between water and rock under the pressures and temperatures present within these worlds. Investigating the conditions for the homogeneous mixing of these materials is imperative to characterizing bulk properties and evolution of water-rich exoplanets. Here, in this study, we use density functional molecular dynamics simulations to study MgO-H 2 O mixtures at high pressure–temperature conditions where H 2 O occurs in solid, superionic, or liquid form. MgO, the representative rocky material, can be either solid or liquid. We start from 500 K at 120 GPa, increasing the temperature step by step up to 8000 K. By inspection, we determine the temperature at which MgO-HO homogeneously mix in our simulations. At 6000 K and 174 GPa is when we find the system to homogeneously mix. This heat-until-it-mixes approach provides us with an upper bound on the temperature for the mixing of MgO and H 2 O. We find that homogeneous mixing occurs at sufficiently low temperatures to be relevant for the collisional growth of a water-rich planet.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

ReactionMechanismSimulator.jl: A modern approach to chemical kinetic mechanism simulation and analysis

Abstract We present ReactionMechanismSimulator.jl (RMS), a modern differentiable software for the simulation and analysis of chemical kinetic mechanisms, including multiphase systems. RMS has already been applied to problems in combustion, pyrolysis, polymers, pharmaceuticals, catalysis, and electrocatalysis. RMS is written in Julia, making it easy to develop and allowing it to take advantage of Julia's extensive numerical computing ecosystem. In addition to its extensive library of optimized analytic Jacobians, RMS can generate and use Jacobians computed using automatic differentiation and symbolically generated analytic Jacobians. RMS is demonstrated to be faster than Cantera and Chemkin in several benchmarks. RMS also implements an extensive set of features for analyzing chemical mechanisms, including a library of easy‐to‐call plotting functions, molecular structure resolved flux diagram generation, crash analysis, traditional sensitivity analysis, transitory sensitivity analysis, and an automatic mechanism analysis toolkit. RMS implements efficient adjoint and parallel forward sensitivity analyses. We also demonstrate the ease of adding new features to RMS.

Johnson, Matthew S.↗
DOE OSTI2024

In-Depth Proteome Profiling of the Hippocampus of LDLR Knockout Mice Reveals Alternation in Synaptic Signaling Pathway

The low-density lipoprotein receptor (LDLR) is a major apolipoprotein receptor that regulates cholesterol homeostasis. LDLR deficiency is associated with cognitive impairment by the induction of synaptopathy in the hippocampus. Despite the close relationship between LDLR and neurodegenerative disorders, proteomics research for protein profiling in the LDLR knockout (KO) model remains insufficient. Therefore, understanding LDLR KO-mediated differential protein expression within the hippocampus is crucial for elucidating a role of LDLR in neurodegenerative disorders. In this study, we conducted first-time proteomic profiling of hippocampus tissue from LDLR KO mice using tandem mass tag (TMT)-based MS analysis. LDLR deficiency induces changes in proteins associated with the transport of diverse molecules, and activity of kinase and catalyst within the hippocampus. Additionally, significant alterations in the expression of components in the major synaptic pathways were found. Furthermore, these synaptic effects were verified using a data-independent acquisition (DIA)-based proteomic method. In conclusion, our data will serve as a valuable resource for further studies to discover the molecular function of LDLR in neurodegenerative disorders.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

ALKBH5-Modified HMGB1-STING Activation Contributes to Radiation Induced Liver Disease via Innate Immune Response

Radiation therapy, which is vital for the treatment of primary liver cancer, comes with unavoidable liver injury, which limits its implementation. N6-methyladenosine (m6A) methylation is involved in many molecular functions. However, its role in radiation-induced liver diseases (RILD) remains unknown. Herein, we investigate the role of m6A methylation in RILD.

62 RADIOLOGY AND NUCLEAR MEDICINE↗